Some batch processing chambers have relatively large diameter susceptors (1 m or more) to hold a sufficient number of wafers for processing. The susceptor is rotated in close proximity (3 mm-0.5 mm) to the injector plate which is another large diameter disc-like component. The parallelism between these components is tuned to control the deposition process. Currently, these components are positioned manually, which takes about three hours. The parallelism changes with respect to the susceptor temperature and chamber pressure. Accordingly, there is a need for apparatus and methods to align and control parallelism to meet the tight clearances and impact of changing process parameters.